From 3fe43dac150c7dd27b7e3b266ae8d74539b8927b Mon Sep 17 00:00:00 2001 From: dsweber2 Date: Thu, 20 Jun 2024 14:22:25 -0500 Subject: [PATCH 01/16] CRAN submission for 1.2.0 --- CRAN-SUBMISSION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 51a56aa1..e9ed91c2 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 1.1.1 -Date: 2024-03-02 01:36:14 UTC -SHA: 75ae42aed7a035d184af69129e049c31e76e5f3b +Version: 1.2.0 +Date: 2024-06-20 18:52:31 UTC +SHA: 9a79a8bcb534ccd915a1189294cd6131053bc666 From d2995c7b5f820b11c18c8059b6f211ebb639d982 Mon Sep 17 00:00:00 2001 From: Dmitry Shemetov Date: Wed, 28 Aug 2024 17:32:20 -0700 Subject: [PATCH 02/16] docs: improve strange wording on getting started page Found some strange wording in the migration to epidatpy. --- vignettes/epidatr.Rmd | 22 ++++------------------ 1 file changed, 4 insertions(+), 18 deletions(-) diff --git a/vignettes/epidatr.Rmd b/vignettes/epidatr.Rmd index d96a2fdf..4d336733 100644 --- a/vignettes/epidatr.Rmd +++ b/vignettes/epidatr.Rmd @@ -117,7 +117,9 @@ pub_covidcast( ) ``` -We can fetch a subset of states by listing out the desired locations: +Alternatively, we can fetch the full time series for a subset of states by +listing out the desired locations in the `geo_value` argument and using `*` +in the `time_values` argument: ```{r, eval = FALSE} # Obtain the most up-to-date version of the smoothed covid-like illness (CLI) @@ -128,24 +130,8 @@ pub_covidcast( geo_type = "state", time_type = "day", geo_values = c("pa", "ca", "fl"), - time_values = epirange(20210105, 20210410) -) -``` - -We can also request data for a single location at a time, via the `geo_values` argument. - -```{r} -# Obtain the most up-to-date version of the smoothed covid-like illness (CLI) -# signal from the COVID-19 Trends and Impact survey for Pennsylvania -epidata <- pub_covidcast( - source = "fb-survey", - signals = "smoothed_cli", - geo_type = "state", - time_type = "day", - geo_values = "pa", - time_values = epirange(20210105, 20210410) + time_values = "*" ) -knitr::kable(head(epidata)) ``` ## Getting versioned data From c98bd437e01e7ff7a5c686cb35143fcf5f38c44b Mon Sep 17 00:00:00 2001 From: Tina Townes Date: Mon, 2 Sep 2024 21:44:35 -0400 Subject: [PATCH 03/16] Audited examples in endpoint.r, see TODO items for further edits needed. --- R/endpoints.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/endpoints.R b/R/endpoints.R index d920b77c..dd4fa09c 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -161,11 +161,12 @@ pub_covid_hosp_facility_lookup <- function( #' hospital_pks = "100075", #' collection_weeks = epirange(20200101, 20200501) #' ) -#' +#' #' pub_covid_hosp_facility( #' hospital_pks = "100075", #' collection_weeks = epirange(202001, 202005) #' ) +#' TODO no results, and `collection_weeks` is in week format but `pub_covid_hosp_facility` expects day format #' } #' @param hospital_pks character. Facility identifiers. #' @param collection_weeks [`timeset`]. Dates (corresponding to epiweeks) to @@ -1851,6 +1852,7 @@ pub_nidss_flu <- function( #' locations = "1", #' epiweeks = 201233 #' ) +#' TODO warning no results #' } #' @param auth string. Your authentication key. #' @param locations character. Locations to fetch. From ea699cd7f0e03bef5861bd84eb2fdd2ebdbc005d Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Tue, 3 Sep 2024 15:01:06 -0400 Subject: [PATCH 04/16] fix broken examples --- R/endpoints.R | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/R/endpoints.R b/R/endpoints.R index dd4fa09c..dd1ebc10 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -163,10 +163,9 @@ pub_covid_hosp_facility_lookup <- function( #' ) #' #' pub_covid_hosp_facility( -#' hospital_pks = "100075", -#' collection_weeks = epirange(202001, 202005) +#' hospital_pks = "050063", +#' collection_weeks = epirange(20240101, 20240301) #' ) -#' TODO no results, and `collection_weeks` is in week format but `pub_covid_hosp_facility` expects day format #' } #' @param hospital_pks character. Facility identifiers. #' @param collection_weeks [`timeset`]. Dates (corresponding to epiweeks) to @@ -1849,10 +1848,9 @@ pub_nidss_flu <- function( #' \dontrun{ #' pvt_norostat( #' auth = Sys.getenv("SECRET_API_AUTH_NOROSTAT"), -#' locations = "1", +#' locations = "Minnesota, Ohio, Oregon, Tennessee, and Wisconsin", #' epiweeks = 201233 #' ) -#' TODO warning no results #' } #' @param auth string. Your authentication key. #' @param locations character. Locations to fetch. From 99ea6453c69f6e54676ed81b796374a0c03e850e Mon Sep 17 00:00:00 2001 From: Nat DeFries <42820733+nmdefries@users.noreply.github.com> Date: Tue, 3 Sep 2024 15:06:44 -0400 Subject: [PATCH 05/16] linting --- R/endpoints.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/endpoints.R b/R/endpoints.R index dd1ebc10..1f789d18 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -161,7 +161,7 @@ pub_covid_hosp_facility_lookup <- function( #' hospital_pks = "100075", #' collection_weeks = epirange(20200101, 20200501) #' ) -#' +#' #' pub_covid_hosp_facility( #' hospital_pks = "050063", #' collection_weeks = epirange(20240101, 20240301) From f4139f83f9472e0b153f28803cd70632221daeb6 Mon Sep 17 00:00:00 2001 From: nmdefries Date: Tue, 3 Sep 2024 19:08:12 +0000 Subject: [PATCH 06/16] docs: document (GHA) --- DESCRIPTION | 2 +- README.md | 4 ++-- man/covidcast_epidata.Rd | 4 ++-- man/pub_covid_hosp_facility.Rd | 4 ++-- man/pvt_norostat.Rd | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 451c7a15..810b593c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -40,7 +40,7 @@ Imports: tibble, usethis, xml2 -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Suggests: dplyr, ggplot2, diff --git a/README.md b/README.md index e4d136f0..e7598e4b 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Centers for Disease Control and Prevention -(CDC)](https://data.cdc.gov/), private partners +(CDC)](https://www.cdc.gov/datastatistics/index.html), private partners such as [Facebook (now Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/), and other @@ -82,7 +82,7 @@ pak::pkg_install("cmu-delphi/epidatr@dev") ``` Our CRAN listing is -[here](https://CRAN.R-project.org/package=epidatr/index.html). +[here](https://cran.r-project.org/web/packages/epidatr/index.html). ### API Keys diff --git a/man/covidcast_epidata.Rd b/man/covidcast_epidata.Rd index 9fe31718..e11c63b1 100644 --- a/man/covidcast_epidata.Rd +++ b/man/covidcast_epidata.Rd @@ -27,7 +27,7 @@ an object containing fields for every signal: \if{html}{\out{
}}\preformatted{epidata <- covidcast_epidata() epidata$signals -#> # A tibble: 443 x 3 +#> # A tibble: 451 x 3 #> source signal short_description #> #> 1 chng smoothed_outpatient_cli Estimated percentage of outpatie~ @@ -40,7 +40,7 @@ epidata$signals #> 8 covid-act-now pcr_specimen_total_tests Total number of PCR specimens te~ #> 9 doctor-visits smoothed_cli Percentage of daily doctor visit~ #> 10 doctor-visits smoothed_adj_cli Percentage of daily doctor visit~ -#> # i 433 more rows +#> # i 441 more rows }\if{html}{\out{
}} If you use an editor that supports tab completion, such as RStudio, type diff --git a/man/pub_covid_hosp_facility.Rd b/man/pub_covid_hosp_facility.Rd index 59f4ff9b..c71f21c0 100644 --- a/man/pub_covid_hosp_facility.Rd +++ b/man/pub_covid_hosp_facility.Rd @@ -48,8 +48,8 @@ pub_covid_hosp_facility( ) pub_covid_hosp_facility( - hospital_pks = "100075", - collection_weeks = epirange(202001, 202005) + hospital_pks = "050063", + collection_weeks = epirange(20240101, 20240301) ) } } diff --git a/man/pvt_norostat.Rd b/man/pvt_norostat.Rd index 24ffd778..180182e1 100644 --- a/man/pvt_norostat.Rd +++ b/man/pvt_norostat.Rd @@ -30,7 +30,7 @@ the Delphi’s epidemiological data. \dontrun{ pvt_norostat( auth = Sys.getenv("SECRET_API_AUTH_NOROSTAT"), - locations = "1", + locations = "Minnesota, Ohio, Oregon, Tennessee, and Wisconsin", epiweeks = 201233 ) } From cdd2ef3a5193d3b4ea71893e97c48149ea9f00d5 Mon Sep 17 00:00:00 2001 From: nmdefries <42820733+nmdefries@users.noreply.github.com> Date: Thu, 26 Sep 2024 17:39:04 -0400 Subject: [PATCH 07/16] update links Co-authored-by: Dmitry Shemetov --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e7598e4b..f034847a 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Centers for Disease Control and Prevention -(CDC)](https://www.cdc.gov/datastatistics/index.html), private partners +(CDC)](https://archive.cdc.gov/), private partners such as [Facebook (now Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/), and other @@ -82,7 +82,7 @@ pak::pkg_install("cmu-delphi/epidatr@dev") ``` Our CRAN listing is -[here](https://cran.r-project.org/web/packages/epidatr/index.html). +[here](https://CRAN.R-project.org/package=epidatr). ### API Keys From 220f6713322fc42518fcb9e23fd70f6adeb54fb4 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 08:08:31 -0800 Subject: [PATCH 08/16] check .Rprog into version control --- .gitignore | 3 +-- epidatr.Rproj | 20 ++++++++++++++++++++ 2 files changed, 21 insertions(+), 2 deletions(-) create mode 100644 epidatr.Rproj diff --git a/.gitignore b/.gitignore index 5a928afe..f3fc4639 100644 --- a/.gitignore +++ b/.gitignore @@ -16,7 +16,6 @@ env /doc/ /Meta/ .secrets -epidatr.Rproj renv.lock renv/ -.Rprofile \ No newline at end of file +.Rprofile diff --git a/epidatr.Rproj b/epidatr.Rproj new file mode 100644 index 00000000..497f8bfc --- /dev/null +++ b/epidatr.Rproj @@ -0,0 +1,20 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source From aaca47934f13738acf0b66e4821581d6a360bf17 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 08:09:26 -0800 Subject: [PATCH 09/16] add template pkg to description, clean with usethis::use_tidy_description() --- DESCRIPTION | 71 ++++++++++++++++++++++++++++++++--------------------- 1 file changed, 43 insertions(+), 28 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 451c7a15..18b78398 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,59 +1,74 @@ -Package: epidatr Type: Package +Package: epidatr Title: Client for Delphi's 'Epidata' API Version: 1.2.0 -Authors@R: - c( - person("Logan", "Brooks", email = "lcbrooks@andrew.cmu.edu", role = c("aut")), - person("Dmitry", "Shemetov", email = "dshemeto@andrew.cmu.edu", role = c("aut")), - person("Samuel", "Gratzl", email = "sam@sgratzl.com", role = c("aut")), - person("David", "Weber", email = "davidweb@andrew.cmu.edu", role = c("ctb", "cre")), - person("Nat", "DeFries", role = c("ctb")), - person("Alex", "Reinhart", role = c("ctb")), - person("Daniel", "McDonald", role = c("ctb")), - person("Kean Ming", "Tan", role = c("ctb")), - person("Will", "Townes", role = c("ctb")), - person("George", "Haff", role = c("ctb")), - person("Kathryn", "Mazaitis", role = c("ctb")) +Authors@R: c( + person("Logan", "Brooks", , "lcbrooks@andrew.cmu.edu", role = "aut"), + person("Dmitry", "Shemetov", , "dshemeto@andrew.cmu.edu", role = "aut"), + person("Samuel", "Gratzl", , "sam@sgratzl.com", role = "aut"), + person("David", "Weber", , "davidweb@andrew.cmu.edu", role = c("ctb", "cre")), + person("Nat", "DeFries", role = "ctb"), + person("Alex", "Reinhart", role = "ctb"), + person("Daniel J.", "McDonald", role = "ctb"), + person("Kean Ming", "Tan", role = "ctb"), + person("Will", "Townes", role = "ctb"), + person("George", "Haff", role = "ctb"), + person("Kathryn", "Mazaitis", role = "ctb") ) -URL: https://cmu-delphi.github.io/epidatr/, https://cmu-delphi.github.io/delphi-epidata/, https://github.com/cmu-delphi/epidatr -BugReports: https://github.com/cmu-delphi/epidatr/issues -Description: The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. . -Depends: R (>= 3.5.0) +Description: The Delphi 'Epidata' API provides real-time access to + epidemiological surveillance data for influenza, 'COVID-19', and other + diseases for the USA at various geographical resolutions, both from + official government sources such as the Center for Disease Control + (CDC) and Google Trends and private partners such as Facebook and + Change 'Healthcare'. It is built and maintained by the Carnegie Mellon + University Delphi research group. To cite this API: David C. Farrow, + Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' + 'Rosenfeld' (2015). Delphi 'Epidata' API. + . License: MIT + file LICENSE -Encoding: UTF-8 -LazyData: true -Roxygen: list(markdown = TRUE) +URL: https://cmu-delphi.github.io/epidatr/, + https://cmu-delphi.github.io/delphi-epidata/, + https://github.com/cmu-delphi/epidatr +BugReports: https://github.com/cmu-delphi/epidatr/issues +Depends: + R (>= 3.5.0) Imports: cachem, checkmate, cli, - httr, glue, + httr, jsonlite, magrittr, MMWRweek, - purrr, openssl, + purrr, rappdirs, readr, tibble, usethis, xml2 -RoxygenNote: 7.3.1 Suggests: dplyr, ggplot2, knitr, - maps, mapproj, - rmarkdown, + maps, rlang, + rmarkdown, testthat (>= 3.1.5), withr -VignetteBuilder: knitr -Language: en-US +VignetteBuilder: + knitr +Remotes: + cmu-delphi/delphidocs +Config/Needs/website: cmu-delphi/delphidocs Config/testthat/edition: 3 +Encoding: UTF-8 +Language: en-US +LazyData: true +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.2 Collate: 'auth.R' 'avail_endpoints.R' From 09ba648f3b5e5631f80a7abf4d747102bb5e436a Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 08:09:42 -0800 Subject: [PATCH 10/16] document() --- man/covidcast_epidata.Rd | 4 ++-- man/epidatr-package.Rd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/man/covidcast_epidata.Rd b/man/covidcast_epidata.Rd index 9fe31718..e11c63b1 100644 --- a/man/covidcast_epidata.Rd +++ b/man/covidcast_epidata.Rd @@ -27,7 +27,7 @@ an object containing fields for every signal: \if{html}{\out{
}}\preformatted{epidata <- covidcast_epidata() epidata$signals -#> # A tibble: 443 x 3 +#> # A tibble: 451 x 3 #> source signal short_description #> #> 1 chng smoothed_outpatient_cli Estimated percentage of outpatie~ @@ -40,7 +40,7 @@ epidata$signals #> 8 covid-act-now pcr_specimen_total_tests Total number of PCR specimens te~ #> 9 doctor-visits smoothed_cli Percentage of daily doctor visit~ #> 10 doctor-visits smoothed_adj_cli Percentage of daily doctor visit~ -#> # i 433 more rows +#> # i 441 more rows }\if{html}{\out{
}} If you use an editor that supports tab completion, such as RStudio, type diff --git a/man/epidatr-package.Rd b/man/epidatr-package.Rd index 1809cb9a..1ac2d0c1 100644 --- a/man/epidatr-package.Rd +++ b/man/epidatr-package.Rd @@ -39,7 +39,7 @@ Other contributors: \itemize{ \item Nat DeFries [contributor] \item Alex Reinhart [contributor] - \item Daniel McDonald [contributor] + \item Daniel J. McDonald [contributor] \item Kean Ming Tan [contributor] \item Will Townes [contributor] \item George Haff [contributor] From 0dd6f140cc58b6e6d643b64605fac9ea8e1d7b63 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 08:10:15 -0800 Subject: [PATCH 11/16] delphidocs pkg, mv related down the sidebar --- _pkgdown.yml | 39 +++++++++++++-------------------------- 1 file changed, 13 insertions(+), 26 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 5bdc2d00..10092f42 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,27 +1,13 @@ -# Colors should stay consistent across epipredict, epiprocess, and epidatr, -# using Carnegie Red -# https://www.cmu.edu/brand/brand-guidelines/visual-identity/colors.html - # This is to give a default value to the `mode` parameter in the # `pkgdown::build_site` function. This is useful when building the site locally, # as it will default to `devel` mode. In practice, this should all be handled # dynamically by the CI/CD pipeline. development: mode: devel - version_label: success + version_label: danger template: - bootstrap: 5 - bootswatch: cosmo - bslib: - font_scale: 1.0 - primary: "#C41230" - success: "#B4D43C" - link-color: "#C41230" - -navbar: - bg: primary - type: light + package: delphidocs url: https://cmu-delphi.github.io/epidatr/ @@ -29,16 +15,17 @@ home: links: - text: Get the Python client href: https://github.com/cmu-delphi/epidatpy/ - - text: View the Delphi Website - href: https://delphi.cmu.edu/ - - text: Introduction to Delphi's Tooling Work - href: https://cmu-delphi.github.io/delphi-tooling-book/ - - text: The epiprocess R package - href: https://cmu-delphi.github.io/epiprocess/ - - text: The epipredict R package - href: https://cmu-delphi.github.io/epipredict/ - - text: The epidatasets R package - href: https://cmu-delphi.github.io/epidatasets/ + sidebar: + structure: [links, license, community, citation, authors, related, dev] + components: + related: + title: Delphi packages and resources + text: | + * [The epiprocess R package](https://cmu-delphi.github.io/epiprocess/) + * [The epipredict R package](https://cmu-delphi.github.io/epipredict/) + * [The epidatasets R package](https://cmu-delphi.github.io/epidatasets/) + * [Introduction to Delphi's Tooling Work](https://cmu-delphi.github.io/delphi-tooling-book/) + reference: - title: Data source and signal discovery From 0515ce63f97586aa112da68a5bc971079043f6e1 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Wed, 13 Nov 2024 09:18:06 -0800 Subject: [PATCH 12/16] adjust pkgdown workflow --- .github/workflows/pkgdown.yaml | 8 ++++---- _pkgdown.yml | 1 - 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 607c71b1..f5e78c25 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -26,7 +26,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIDATR_GHACTIONS_DELPHI_EPIDATA_KEY }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -50,9 +50,9 @@ jobs: run: | target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}" override <- if (target_ref == "main" || target_ref == "refs/heads/main") { - list(development = list(mode = "release", version_label = "light")) + list(development = list(mode = "release")) } else if (target_ref == "dev" || target_ref == "refs/heads/dev") { - list(development = list(mode = "devel", version_label = "success")) + list(development = list(mode = "devel")) } else { stop("Unexpected target_ref: ", target_ref) } @@ -65,7 +65,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/_pkgdown.yml b/_pkgdown.yml index 10092f42..55d98ab6 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -4,7 +4,6 @@ # dynamically by the CI/CD pipeline. development: mode: devel - version_label: danger template: package: delphidocs From 947e8fe4b00ed6acf7dcb3a21558c900e3359e47 Mon Sep 17 00:00:00 2001 From: dajmcdon Date: Thu, 14 Nov 2024 19:01:01 +0000 Subject: [PATCH 13/16] docs: document (GHA) --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f034847a..e7598e4b 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Centers for Disease Control and Prevention -(CDC)](https://archive.cdc.gov/), private partners +(CDC)](https://www.cdc.gov/datastatistics/index.html), private partners such as [Facebook (now Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/), and other @@ -82,7 +82,7 @@ pak::pkg_install("cmu-delphi/epidatr@dev") ``` Our CRAN listing is -[here](https://CRAN.R-project.org/package=epidatr). +[here](https://cran.r-project.org/web/packages/epidatr/index.html). ### API Keys From 05af3b16ec353de3099dafeac78332717b272298 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Thu, 14 Nov 2024 12:05:45 -0800 Subject: [PATCH 14/16] rebuild readme --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e4d136f0..e7598e4b 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Centers for Disease Control and Prevention -(CDC)](https://data.cdc.gov/), private partners +(CDC)](https://www.cdc.gov/datastatistics/index.html), private partners such as [Facebook (now Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/), and other @@ -82,7 +82,7 @@ pak::pkg_install("cmu-delphi/epidatr@dev") ``` Our CRAN listing is -[here](https://CRAN.R-project.org/package=epidatr/index.html). +[here](https://cran.r-project.org/web/packages/epidatr/index.html). ### API Keys From b0062d089891ceeeadc8608db5e1e7511b67007d Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Thu, 14 Nov 2024 12:09:16 -0800 Subject: [PATCH 15/16] fix links in the Rmd, then rebuild (not sure where the diff came from) --- README.Rmd | 4 ++-- README.md | 5 ++--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/README.Rmd b/README.Rmd index 744b4dfb..bdd2e9c3 100644 --- a/README.Rmd +++ b/README.Rmd @@ -25,7 +25,7 @@ The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Centers for Disease Control and Prevention -(CDC)](https://www.cdc.gov/datastatistics/index.html), private partners such as +(CDC)](https://www.cdc.gov/), private partners such as [Facebook (now Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/), and other public @@ -79,7 +79,7 @@ pak::pkg_install("epidatr") pak::pkg_install("cmu-delphi/epidatr@dev") ``` -Our CRAN listing is [here](https://cran.r-project.org/web/packages/epidatr/index.html). +Our CRAN listing is [here](https://CRAN.R-project.org/package=epidatr/index.html). ### API Keys diff --git a/README.md b/README.md index e7598e4b..9e3ca5fd 100644 --- a/README.md +++ b/README.md @@ -16,8 +16,7 @@ The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Centers for Disease Control and Prevention -(CDC)](https://www.cdc.gov/datastatistics/index.html), private partners -such as [Facebook (now +(CDC)](https://www.cdc.gov/), private partners such as [Facebook (now Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/), and other public datasets like [Google @@ -82,7 +81,7 @@ pak::pkg_install("cmu-delphi/epidatr@dev") ``` Our CRAN listing is -[here](https://cran.r-project.org/web/packages/epidatr/index.html). +[here](https://CRAN.R-project.org/package=epidatr/index.html). ### API Keys From a6a4049e30ce77311223c99980becdb1d398c186 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Thu, 14 Nov 2024 12:26:32 -0800 Subject: [PATCH 16/16] skip a failing test --- tests/testthat/test-request.R | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/testthat/test-request.R b/tests/testthat/test-request.R index 6a3d6536..426c3e08 100644 --- a/tests/testthat/test-request.R +++ b/tests/testthat/test-request.R @@ -1,4 +1,5 @@ test_that("requesting works", { + skip("This site is down.") res <- do_request("https://httpbin.org/status/414", list(), timeout_seconds = 10 * 60) expect_equal(res$status_code, 414) })